A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways

Lourenço, Anália; Carneiro, Sônia Maria Marchiorato; Pinto, José P.; Rocha, Miguel; Ferreira, E. C.; Rocha, Isabel

doi:10.1515/jib-2011-183

Cited by 10 publications

(11 citation statements)

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“…The second most abundant pathway corresponds to Transport, Inner Membrane, which again is in agreement with Ref. and Ref. .…”

Section: Resultssupporting

confidence: 90%

“…The most prominent pathway is Alternate Carbon Metabolism, in agreement with Ref. , where the authors found that Alternate Carbon Metabolism is related to genes whose expression depends on external stimuli, particularly on alteration of carbon sources. It is also in agreement with results in Ref.…”

Section: Resultssupporting

confidence: 86%

“…This permits the construction of a super significant flux backbone that comprises all the links in the SFB in each different media and in which each contributing SFB has uniform representation in fraction of links. This leads to the identification of pathways whose associated reactions are potentially more sensitive to changes in the environment, unveiling Alternate Carbon Metabolism as the pathway with more capabilities to respond to external stimuli, in accordance with existing works . This finding could also be seen as a successful positive control for the methodology applied here.…”

Section: Discussionsupporting

confidence: 83%

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Detecting the Significant Flux Backbone of Escherichia coli metabolism

2017

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The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of Escherichia coli, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In E. coli, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints.Keywords: disparity filter; flux balance analysis; metabolic backbones; metabolic networks High-quality genome-scale metabolic reconstructions are composed of thousands of reactions and metabolites [1][2][3][4]. Due to their complexity, the analysis of these metabolic reconstructions requires computational approaches, like constraint-based optimization techniques [5,6], and methodological frameworks, like complex network science [7,8] Backbones maintain significant information while displaying a substantially decreased number of interconnections and, hence, can provide accurate but reduced versions of the whole system. In this direction, the work by Almaas et al.[13] introduced a filtering technique that selects the reactions dominating the production and consumption of each metabolite and connects two metabolites if the reaction producing one of them with the highest flux happens to be the reaction consuming the other with the highest flux, which defines a high-flux backbone. This method is able to segregate classical pathways, but the selected high-flux subgraphs present a

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“…The second most abundant pathway corresponds to Transport, Inner Membrane, which again is in agreement with Ref. and Ref. .…”

Section: Resultssupporting

confidence: 90%

Section: Resultssupporting

confidence: 86%

Section: Discussionsupporting

confidence: 83%

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Detecting the Significant Flux Backbone of Escherichia coli metabolism

2017

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“…(2018) E3S Web of Conferences https://doi.org/10.1051/e3sconf /20186801006 68 100 1 st SRICOENV 2018 6 most concerned bacterial contamination in food handlers is Escherichia coli [7][11] [16][17][18][19] and Staphylococcus aureus [5] [18][19].…”

Section: Introductionmentioning

confidence: 99%

Bacterial Contamination of Food Handlers in X Hospital Palembang

et al. 2018

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The food handlers in Hospital with the bad personal hygiene could be a potential source of infection of a pathogenic organism. The responsibility of hospital food handlers is greater compared with the common food handlers such as in restaurants, etc. This is because they should provide the healthy food to the patients in Hospital who might have low immunity, and the contaminated food could have very dangerous consequences. This study aimed to investigate the potential contamination of food handlers in X hospital, Palembang. The study was carried out by a cross-sectional method on food handlers’. There were 30 respondents examined in this study. The bacterial examination was conducted by following the standard procedures of World Health Organization (WHO). The results showed that there were 11 (36.7%) from 30respondents positively contaminated by Escherichia coliand there all respondent contaminated in samples were women. There was no worker contaminated by Staphylococcus aureus. The study proved that in X hospital of Palembang, there were some food handlers contaminated by Escherichia coli.

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“…Such 'metabolic regulation' provides a fast response to acute extracellular and intracellular perturbations and helps the cell to control the metabolic and Gibbs energy balance. The distribution of different types of regulation of the metabolism of organisms such as Escherichia coli [44,45] and yeast [46] over metabolic, signalling and gene expression has been studied intensively. A comprehensive review [47] outlined the regulation of important metabolic tasks at different levels, including nutrient uptake, energy and amino acid metabolism, and protein synthesis, and highlighted a set of metabolites that carry out specific regulatory functions.…”

Section: Introductionmentioning

confidence: 99%

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

Murabito

Westerhoff

2016

J. R. Soc. Interface.

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Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

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A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways

Cited by 10 publications

References 0 publications

Detecting the Significant Flux Backbone of Escherichia coli metabolism

Detecting the Significant Flux Backbone of Escherichia coli metabolism

Bacterial Contamination of Food Handlers in X Hospital Palembang

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

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